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Open data
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Basic information
Entry | Database: PDB / ID: 6xmp | ||||||
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Title | Structure of P5A-ATPase Spf1, Apo form | ||||||
![]() | P5A-type ATPase | ||||||
![]() | TRANSPORT PROTEIN / P-type ATPase / transmembrane helix dislocase / protein quality control / endoplasmic reticulum | ||||||
Function / homology | ![]() extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / sterol homeostasis / intracellular manganese ion homeostasis / Ion transport by P-type ATPases / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / protein hexamerization ...extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / sterol homeostasis / intracellular manganese ion homeostasis / Ion transport by P-type ATPases / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / protein hexamerization / phosphatidylinositol-4-phosphate binding / protein unfolding / transmembrane transport / intracellular calcium ion homeostasis / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Park, E. / Sim, S.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase. Authors: Michael J McKenna / Sue Im Sim / Alban Ordureau / Lianjie Wei / J Wade Harper / Sichen Shao / Eunyong Park / ![]() Abstract: Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A- ...Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A-adenosine triphosphatase (ATPase) transporter ATP13A1 (Spf1 in yeast) directly interacted with the transmembrane segment (TM) of mitochondrial tail-anchored proteins. P5A-ATPase activity mediated the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Spf1 revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an α-helical TM. Our results indicate that the P5A-ATPase could dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TM dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.4 KB | Display | ![]() |
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PDB format | ![]() | 165.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22260MC ![]() 6xmqC ![]() 6xmsC ![]() 6xmtC ![]() 6xmuC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 137573.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Description: chromosomal SPF1 tagged with a TEV-GFP-tag / Production host: ![]() ![]() References: UniProt: P39986, Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate | ||
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#2: Sugar | ChemComp-LMT / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: P5A-ATPase Spf1 Apo form / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 776554 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143694 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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